Phytophthora infestans vs Phytophthora ramorum Translated Blat Results

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Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Phytophthora infestans was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 185,009

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans T30-4

Uncovered: 193,173,229 out of 228,543,505
Covered: 35,370,276 out of 228,543,505

Uncovered: 3,919,873 out of 22,421,425
Matches: 14,503,026 out of 22,421,425
Mismatches: 3,974,416 out of 22,421,425
Insertions: 24,110 out of 22,421,425

Phytophthora ramorum

Uncovered: 46,179,068 out of 66,652,401
Covered: 20,473,333 out of 66,652,401

Uncovered: 7,396,927 out of 22,377,278
Matches: 11,812,940 out of 22,377,278
Mismatches: 3,135,751 out of 22,377,278
Insertions: 31,660 out of 22,377,278

Configuration parameters

ParameterValue
Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

Phytophthora infestans Phytophthora ramorum
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}